Team:UANL Mty-Mexico/Project/The Code

From 2011.igem.org

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{{:Team:UANL_Mty-Mexico/Templates/Banner-template}}
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{{:Team:UANL_Mty-Mexico/Templates/Menu-template}}
<html>
<html>
<head>
<head>
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/-->
/-->
-
        <!-- Include jQuery first. -->
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-
<script type="text/javascript" src="http://www.genobiotec2011.org/iGEMwiki/jquery-1.3.2.min.js"></script>
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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  <title>Team: UANL_Mty-Mexico</title>
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        <!-- Include the below script, Copyright 2010, Brandon Aaron (http://brandonaaron.net/) for scrollwheel support. -->
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<script type="text/javascript" src="http://www.genobiotec2011.org/iGEMwiki/jquery-mousewheel/jquery.mousewheel.min.js"></script>
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-
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<link rel="stylesheet" type="text/css" href="http://www.genobiotec2011.org/iGEMwiki/slidedeck.skin.css" media="screen" />
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-
        <!-- Styles for the skin that only load for Internet Explorer -->
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        <!--[if lte IE 8]>
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        <link rel="stylesheet" type="text/css" href="http://www.genobiotec2011.org/iGEMwiki/slidedeck.skin.ie.css" media="screen,handheld" />
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-
        <![endif]-->
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-
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        <!-- Include the SlideDeck jQuery script. -->
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<script type="text/javascript" src="http://www.genobiotec2011.org/iGEMwiki/slidedeck.jquery.lite.pack.js"></script>
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-
       
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        <style type="text/css">
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            #slidedeck_frame {
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width: 665px;
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height: 200px;
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            }       
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        </style>
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<style>
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-
 
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#botonera {
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}
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.lateral-button {
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bold;
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color: #036;
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text-decoration: none;
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padding-top: 10px;
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padding-bottom: 10px;
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padding-left: 10px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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-moz-border-radius: 5px;
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  border-radius: 5px;
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  cursor: pointer;
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  text-align: center;
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}
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.lateral-button:hover {
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bolder;
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color: #036;
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text-decoration:underline;
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background-color:#CCC;
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color:#000;
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padding-top: 10px;
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padding-bottom: 10px;
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padding-left: 10px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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-moz-border-radius: 5px;
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  border-radius: 5px;
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  cursor: pointer;
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  text-align: center;
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}
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.lateral-button a {
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bold;
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color: #036;
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text-decoration: none;
+
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+
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padding-top: 10px;
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padding-bottom: 10px;
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padding-left: 10px;
+
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padding-right: 10px;
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margin: 2px;
+
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-webkit-border-radius: 5px;
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-moz-border-radius: 5px;
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-
  border-radius: 5px;
+
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  cursor: pointer;
+
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  text-align: center;
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}
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+
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.lateral-button:hover a {
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bolder;
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color: #036;
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text-decoration:underline;
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background-color:#CCC;
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color:#000;
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+
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padding-top: 10px;
+
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padding-bottom: 10px;
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padding-left: 10px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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-moz-border-radius: 5px;
+
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  border-radius: 5px;
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  cursor: pointer;
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  text-align: center;
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}
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.style5.top-menu {
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  background: transparent;
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  margin: auto;
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  width: 950px;
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  margin-top: -35px;
+
    
    
-
}
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<META NAME="keywords" CONTENT="UANL,iGEM,Universidad,Autonoma,Nuevo,Leon,Biphasic,switch,Lambda,Genetic,Regulation,Quorum,Sensing,pRM,OL,Green Light,Red Light">
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.style5 ul.top-menu-main {
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<META NAME="description" CONTENT="iGEM-UANL is the representative team from Universidad Autonoma de Nuevo León, at Monterrey, México. This team is composed of ten students who spent their summer in the lab, having fun with transformations, constructions and plasmidic DNA extractions. This">
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  margin: auto;
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<META NAME="abstract" CONTENT="Information processing through living things remains a challenge to science. Genetic logic-gates and">
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  width: 950px;
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<META NAME="author" CONTENT="iGEM-UANL">
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  font-family: Georgia, Tahoma, Arial;
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<META NAME="robots" CONTENT="FOLLOW,INDEX">
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  font-size: 10px;
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  line-height: 18px;
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<link href="http://www.asebiogen.org/igemuanl/mainStyle.css" rel="stylesheet" type="text/css">
-
}
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.style5 ul.top-menu-main > li {
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  background: #000;
+
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  border-right: 1px solid #afafaf;
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-
 
 
-
  color: #fff;
 
-
  margin: 0;
 
-
}
 
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.style5 ul.top-menu-main > li.last {
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<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
-
  border-right: none;
+
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}
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.style5 ul.top-menu-main > li:hover .menu-item-text
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{color: #cfcfcf; text-shadow: 0 1px 0 #0C131C;}
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.style5 ul.top-menu-main > li:hover{
 
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  background: #333 transparent;
 
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  color: #fff;
 
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  -moz-box-shadow: 0 0 8px #333;
 
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  -webkit-box-shadow: 0 0 8px #333;
 
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  box-shadow: 0 0 8px #333;
 
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}
 
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.style5 ul.top-menu-main > li > a {
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<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
-
  color: #fff;
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  text-decoration: none;
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}
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.style5 ul.top-menu-main > li > a:hover {
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  color: #fff;
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}
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.style5 ul.top-menu-main > li > a {
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<script type='text/javascript' src='http://www.asebiogen.org/igemuanl/jquery.easing.1.3.js'></script>
-
  padding: 10px 10px;
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<script type='text/javascript' src='http://www.asebiogen.org/igemuanl/query.slideup.menu.1.0.min.js'></script>
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}
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.style5 ul.top-submenu {
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  -moz-box-shadow: 0 0 8px #333;
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  -webkit-box-shadow: 0 0 8px #333;
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  /*box-shadow: 0 0 8px #333;*/
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  box-shadow: 0 0 8px #fff;
+
    
    
-
}
+
 
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<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery.scroll-follow.js"></script>  
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.style5 ul.top-submenu > li {
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  margin: 0px;
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  padding: 5px 10px;
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}
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.style5 ul.top-submenu > li a {
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}
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.style5 ul.top-submenu > li.hover {
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.style5 ul.top-submenu > li a:hover {
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  background: #000 ;
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  color: #fff;
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}
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+
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-
/* Wiki Hacks - START */
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-
/* Author: Pieter van Boheemen */
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-
/* Team: TU Delft */
+
-
 
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-
#globalWrapper { background-color: transparent; border: none; margin: 0; padding: 0; width: 100%; height:100%;}
+
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+
-
#content { background-color: transparent; border: none; padding: 0; margin: 0; width: 100%; overflow: hidden; height:100%;}
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#bodyContent { border: none; padding:0; margin:0; width:100%; height:100%;}
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#top-section { height: 0px; margin: 0px; margin-left: auto; margin-right: auto; margin-bottom: 0 !important;
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padding:0; border: none; font-size: 10px}
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#p-logo { height:1px; overflow:hidden; display: none;}
+
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+
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#search-controls { overflow:hidden; display:block; background: none; position: absolute; top: 100px; right: 40px;}
+
-
 
+
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/*
+
-
.left-menu { width: 500px !important; display:block; margin-top:-80px; border: none; text-align: right;}
+
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.left-menu ul { border: none; }
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#menubar.right-menu { width:300px; display:block; float:left; margin-top:-80px; border: none;}
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.right-menu ul { border: none; width: 300px;}
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*/
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#footer-box { background-image: url(http://www.genobiotec2011.org/iGEMwiki/images/back.jpg); background-color: #000000; width: 100%; margin: -10px; padding: 20px 0; display: none;}
+
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+
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.visualClear { display: none; }
+
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+
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#search-controls { display:none; }
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+
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h3#siteSub { display: none;}
+
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#contentSub {display: none;}
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//p:first-child { display: none;}
+
-
 
+
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+
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#footer { border: none; width: 965px; margin: 0 auto; padding: 0;}
+
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.firstHeading { display: none;}
+
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#f-list a { color: #333; font-size: 10px;}
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#f-list a:hover { color: #666; height: 100px;}
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.printfooter { display: none; }
+
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#footer ul { margin: 0; padding: 0;}
+
-
#footer ul li { margin-top: 0; margin-bottom: 0; margin-left: 10px; margin-right: 10px; padding: 0;}
+
-
/* Wiki Hacks - END */
+
-
 
+
-
 
+
-
body {
+
-
margin: 0;
+
-
padding: 0;
+
-
color: #333;
+
-
font-family: tahoma, arial;
+
-
font-size: 10px;
+
-
background-color: #333;
+
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background-image: url(images/back.jpg);
+
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}
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a {
+
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color: #fff;
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text-decoration: none;
+
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font-size: 10px;
+
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}
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/* float clearing for IE6 */
+
-
* html .clearfix{
+
-
  height: 1%;
+
-
  overflow: visible;
+
-
}
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-
 
+
-
/* float clearing for IE7 */
+
-
*+html .clearfix{
+
-
  min-height: 1%;
+
-
}
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-
 
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-
/* float clearing for everyone else */
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+
-
clear: both;
+
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content: ".";
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display: block;
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-
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+
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}
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ul.top-menu-main {
+
-
  margin: auto;
+
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  width: 800px;
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}
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ul.top-menu-main > li {
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}
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-
  font-family: "Arial Narrow", Georgia, Tahoma, arial;
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  text-transform: uppercase;
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  font-weight: bold;
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+
-
  height: 37px;
+
-
  border-bottom: 1px solid #333;
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}
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.header {
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width: 964px;
+
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margin: auto;
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width: 964px;
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margin: auto;
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background-color: #FFF;
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font-size: 12px;
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z-index: 10;
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-
  padding: 10px;
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  position: relative; float: left; width : 700px;
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}
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.s-menu {
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padding: 0;
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margin-top: 20px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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-moz-border-radius: 5px;
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border-radius: 5px;
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cursor: pointer;
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text-align: center;
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color: #036;
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font-size: 12px;
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text-align: center;
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font-size: 12px;
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}
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-
 
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-
 
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-
 
+
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.col-1-3 {
+
-
width: 200;
+
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/*margin-right: 2%;*/
+
-
position: relative;
+
-
float: right;
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font-size: 12px;
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color: #FFF;
+
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font-weight: bold;
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text-decoration: none;
+
 +
<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/slimbox2/js/slimbox2.js"></script>
-
}
+
  <script type="text/javascript">  
-
 
+
  $( document ).ready( function ()
-
 
+
{
-
 
+
$( '#rightColumn' ).scrollFollow();
-
 
+
}
-
.sidebar1 {
+
);
-
float: left;
+
  </script>  
-
width: 180px;
+
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background: #EADCAE;
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padding-bottom: 10px;
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}
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.sidebar2 {
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float: right;
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width: 180px;
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background: #EADCAE;
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padding-bottom: 10px;
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}
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text-align: justify;
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font-size: 20px;
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}
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#footer-leftColumn {
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float:left;
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width:317px;
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padding-left: 0px;
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text-align: left;
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padding-top: 0;
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}
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#footer-middleColumn {
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float:left;
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width:330px;
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padding-left: 0px;
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text-align: center;
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padding-top: 0;
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}
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+
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#footer-rightColumn {
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float:right;
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width:260px;
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padding-left: 0px;
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text-align: right;
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padding-top: 0;
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padding-right: 0;
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}
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#twitter-box {
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text-align:center;
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}
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#leftColumn {
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float:left;
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width:700px;
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text-align: justify;
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padding-top: 10px;
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padding-right: 0px;
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float:right;
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width:200px;
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text-align: center;
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}
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#social-div {
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text-align: right;
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float:right;
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}
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     <div class="br2"></div><div class="br2"></div><div class="br2"></div>             
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     <div id="leftColumn">
     <div id="leftColumn">
 +
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 +
            Project: The Code
 +
    </div>
 +
 +
<div class="br"></div><div class="br"></div>
 +
<div class="br"></div><div class="br"></div>
     <div id="header-project-column">
     <div id="header-project-column">
-
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+
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 +
<div class="br2"></div>
 +
<div class="br2"></div>
           <a name="Code"></a>The Code
           <a name="Code"></a>The Code
-
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+
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 +
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 +
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       </div>
       </div>
     <p>The main idea consists of enabling a bacterial community to interpret a simple code. The code will be composed of just red and green lights. The genetic circuit on which the interpretation relies is not dependent on the nature of the stimuli though, whether light or chemical the information processing remains the same. We use light because it is an elegant non-invasive input.</p>
     <p>The main idea consists of enabling a bacterial community to interpret a simple code. The code will be composed of just red and green lights. The genetic circuit on which the interpretation relies is not dependent on the nature of the stimuli though, whether light or chemical the information processing remains the same. We use light because it is an elegant non-invasive input.</p>
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-
border: 2px solid #036;
 
-
background-color: #FFF;
 
-
}
 
-
</style>
 
<center>
<center>
-
<div id = "img-holder">  
+
<div class = "img-holder" style="width:384px">
-
<img src="http://www.genobiotec2011.org/iGEMwiki/images/Code-fig1.jpg" width="384" height="322" alt="Code-Figure1" align="center">
+
<a href="https://static.igem.org/mediawiki/igem.org/2/26/Code-fig1-1.png"rel="lightbox" title="The Code. Short pulses of a single light will mean message one, while a long continuous pulse will mean a second message. That gives us two messages controlled by each light, summing up to four results. The fifth message will be sent with both lights present at the same time.">
-
 
+
<img src="https://static.igem.org/mediawiki/igem.org/2/26/Code-fig1-1.png" width="384px" height="328px" alt="Code-Figure1" align="center">
-
<span class="img-holder-text"><b>Figure 1.</b> The code. Short pulses of a single light will mean message one, while a long continuous pulse will mean a second message. That gives us two messages controlled by each light, summing up to four results. The fifth message will be sent with both lights present at the same time. </span></div>
+
</a>
 +
<span class="img-holder-text"><b>Figure 1.</b> The code. Short pulses of a single light will mean message one, while a long continuous pulse will mean a second message. That gives us two messages controlled by each light, summing up to four results. The fifth message will be sent with both lights present at the same time. </span>
 +
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</center>
</center>
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font-size:10px;
 
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<p>Constructing the necessary genetic circuitry inside one single cell may be possible but probably much harder to achieve. That being so, we decided to construct the genetic circuit divided in blocks on separate cells that overall interpret the code. We consider this an advantageous approach since compartmentalizing the circuit lowers the construction size and metabolic charge per cell.</p>
<p>Constructing the necessary genetic circuitry inside one single cell may be possible but probably much harder to achieve. That being so, we decided to construct the genetic circuit divided in blocks on separate cells that overall interpret the code. We consider this an advantageous approach since compartmentalizing the circuit lowers the construction size and metabolic charge per cell.</p>
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<p>There will be three kinds of cells with different genotypes, although initially all share the same E. coli strain. Two of them will have similar interpretation mechanisms, which will allow each one to take a single light as input and decide whether to express the first or the second reporter gene included in its genotype (decision that will depend on the code). The third kind of cell will be the one taking the input from both lights to express the last protein. Until now the community managed to control the expression of five fluorescent proteins, however we said each of them should be controlled independently. This is accomplished with cell to cell communication through quorum sensing. The following figure illustrates the way the cells within the community work together:</p>
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<p>There will be three kinds of cells with different genotypes, although initially all share the same <i>E. coli</i> strain. Two of them will have similar interpretation mechanisms, which will allow each one to take a single light as input and decide whether to express the first or the second reporter gene included in its genotype (decision that will depend on the code). The third kind of cell will be the one taking the input from both lights to express the last protein. Until now the community managed to control the expression of five fluorescent proteins, however we said each of them should be controlled independently. This is accomplished with cell to cell communication through quorum sensing. The following figure illustrates the way the cells within the community work together:</p>
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<a href="https://static.igem.org/mediawiki/igem.org/a/a8/800px-Code-fig2.jpg" rel="lightbox" title="The Community. Cells one and two control each the expression of two different fluorescent proteins. Cell three controls the expression of the fifth protein. Independent expression of each of the reporter genes is achieved through quorum sensing. Cells one and two have the capability to send and receive a different QS molecule each (QS1 and QS2 respectively), while cell three is only a receiver. When cell one or two receive an activating message, the production of a QS molecule is activated as well. These molecules will then diffuse through the medium and reach the rest of the cells. The effect of quorum sensing will depend on the receiver. QS2 molecules, when reaching cell one, will unleash the expression of a repressor that will block the production of any of cell's one reporter genes. QS1 molecules will have the same effect on cell two. On the other hand, cell three will be activated only when both QS molecules are present and therefore cells one and two are off. ">
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<span class="img-holder2-text"><b>Figure 2.</b> The community. Cells one and two control each the expression of two different fluorescent proteins. Cell three controls the expression of the fifth protein. Independent expression of each of the reporter genes is achieved through quorum sensing. Cells one and two have the capability to send and receive a different QS molecule each (QS1 and QS2 respectively), while cell three is only a receiver. When cell one or two receive an activating message, the production of a QS molecule is activated as well. These molecules will then diffuse through the medium and reach the rest of the cells. The effect of quorum sensing will depend on the receiver. QS2 molecules, when reaching cell one, will unleash the expression of a repressor that will block the production of any of cell's one reporter genes. QS1 molecules will have the same effect on cell two. On the other hand, cell three will be activated only when both QS molecules are present and therefore cells one and two are off. </span></div>
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</a>
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<span class="img-holder-text"><b>Figure 2.</b> The community. Cells one and two control each the expression of two different fluorescent proteins. Cell three controls the expression of the fifth protein. Independent expression of each of the reporter genes is achieved through quorum sensing. Cells one and two have the capability to send and receive a different QS molecule each (QS1 and QS2 respectively), while cell three is only a receiver. When cell one or two receive an activating message, the production of a QS molecule is activated as well. These molecules will then diffuse through the medium and reach the rest of the cells. The effect of quorum sensing will depend on the receiver. QS2 molecules, when reaching cell one, will unleash the expression of a repressor that will block the production of any of cell's one reporter genes. QS1 molecules will have the same effect on cell two. On the other hand, cell three will be activated only when both QS molecules are present and therefore cells one and two are off. </span></div>
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         <a name="Live"></a>Live Community
         <a name="Live"></a>Live Community
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<p>Here we show an animated explanation for better understanding:</p>
<p>Here we show an animated explanation for better understanding:</p>
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Latest revision as of 16:46, 13 February 2012

banner-main iGEM-logo
Team: UANL_Mty-Mexico
Team: UANL_Mty-Mexico
Project: The Code
The Code

The main idea consists of enabling a bacterial community to interpret a simple code. The code will be composed of just red and green lights. The genetic circuit on which the interpretation relies is not dependent on the nature of the stimuli though, whether light or chemical the information processing remains the same. We use light because it is an elegant non-invasive input.

The message sent to bacteria will depend on the pattern of light. The community should be able to interpret five messages and tell it did it right when expressing a reporter gene. As there will only be two lights, five patterns of them will be used. The five fluorescent proteins available in the Registry (GFP, YFP, RFP, CFP, BFP) fit perfectly to this purpose. The next figure illustrates the five patterns of light that will result in the five different messages sent, each of them represented by the expression of a fluorescent protein.

Code-Figure1 Figure 1. The code. Short pulses of a single light will mean message one, while a long continuous pulse will mean a second message. That gives us two messages controlled by each light, summing up to four results. The fifth message will be sent with both lights present at the same time.
Community

Constructing the necessary genetic circuitry inside one single cell may be possible but probably much harder to achieve. That being so, we decided to construct the genetic circuit divided in blocks on separate cells that overall interpret the code. We consider this an advantageous approach since compartmentalizing the circuit lowers the construction size and metabolic charge per cell.

There will be three kinds of cells with different genotypes, although initially all share the same E. coli strain. Two of them will have similar interpretation mechanisms, which will allow each one to take a single light as input and decide whether to express the first or the second reporter gene included in its genotype (decision that will depend on the code). The third kind of cell will be the one taking the input from both lights to express the last protein. Until now the community managed to control the expression of five fluorescent proteins, however we said each of them should be controlled independently. This is accomplished with cell to cell communication through quorum sensing. The following figure illustrates the way the cells within the community work together:

Code-Figure2 Figure 2. The community. Cells one and two control each the expression of two different fluorescent proteins. Cell three controls the expression of the fifth protein. Independent expression of each of the reporter genes is achieved through quorum sensing. Cells one and two have the capability to send and receive a different QS molecule each (QS1 and QS2 respectively), while cell three is only a receiver. When cell one or two receive an activating message, the production of a QS molecule is activated as well. These molecules will then diffuse through the medium and reach the rest of the cells. The effect of quorum sensing will depend on the receiver. QS2 molecules, when reaching cell one, will unleash the expression of a repressor that will block the production of any of cell's one reporter genes. QS1 molecules will have the same effect on cell two. On the other hand, cell three will be activated only when both QS molecules are present and therefore cells one and two are off.
Live Community

Here we show an animated explanation for better understanding:

OurSymbol

Team: UANL_Mty-Mexico

Retrieved from "http://2011.igem.org/Team:UANL_Mty-Mexico/Project/The_Code"